If you are using Windows MobiPocket Reader to manage your iLiad MOBI files, there is no way to replace the mobipocket logo. This is because MOBI files in the Books/Mobipocket directory (e.g. from Windows MobiPocket Reader) are treated differently from MOBI files anywhere else in the filesystem.

Outside of the Mobipocket directory, the very first time you open a MOBI file it is moved into its own subdirectory with its own manifest.xml file. It is at this point that iRex should extract a cover image from the MOBI file and reference it in the manifest file. They don't do so - probably because they expect everyone to use Windows MobiPocket Reader for their MOBI files. Note that AdamB was able implement book specific cover images for DRM-free LIT files, see Automatic .Lit extractor for the iLiad. I guess this is just one more example of volunteers being able to do so much more than iRex.

Anyway, if you have MOBI files outside of the Mobipocket subdirectory, then as AdamB says you can add your own cover image by editing the manifest.xml file - but only after the file is opened at least once.